The Submarine Pipeline Spans are vulnerable to considerable fatigue damage over its design life period due to the dynamic excitations caused by Vortex Induced Vibration (VIV) in waves and current. In this paper, according to the tried experimentation, the model of vortex-induced vibration in wave and current is proposed. Based on inherent modes determined by the equation of motion describing free vibration, the effect of the cross-flow response and in-line response in the stress of the section of pipeline span, and the impact of the average stress in the fatigue life is considered. By using the theory of spectrum analyses and fatigue analyses, a more reliable method of the fatigue life of submarine pipeline span is proposed. Finally, the effect degree of the average stress is figured out by calculating an example.